The Investigation into the Partnership
by kathrynblack
Summary: Booth is forced to choose between catching the suspect and saving his partner. He makes his choice, but it has unforseen consequences when the F.B.I begins to investigate severing their partnership. Casefile-ish. Slight B/B.
1. Chapter 1

"So, we done here?" Booth asked, standing up to leave, always in a hurry to get out of Sweets' office. Dr. Brennan was right behind him.

"Actually, you two should sit down. There is one more thing, and you're not going to like it. The F.B.I is investigating whether to sever your partnership."

"I thought that's why we're here in the first place, so they don't," Booth said, annoyance clear in his tone.

"Yes and my father is now not in jail," Brennan added, "There's absolutely no reason for them to break us up."

"Remember the incident at the subway station two weeks ago?" Sweets asked.

"That?" Brennan asked, "That was nothing."

"Nothing? Bones they said less than half an inch lower and he would've pierced your jugular, and even I know that'll kill you in a matter of minutes."

"Booth just overreacted," This comment was directed towards Sweets.

"And that Dr. Brennan is exactly what they're problem is," Sweets infromed them, "Starting tomorrow someone will be interviewing the two of you separately, and they will decide whether Dr. Brennan should be assigned a new partner, and Booth be moved somewhere else, or whether you can stay together."

"Moved? Moved as in out of the city?" Booth asked.

"If it comes to that, with Parker in D.C, I should be able to make sure that doesn't happen."

"Can't you just tell them I won't work with another agent," Brennan suggested.

Sweets had already thought of that. "You worked with agent Perotta."

"That was out of necessity, for one case."

"Agent Booth, Dr. Brennan, I have tried everything. Believe me, the Bureau is serious about this."

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Booth tossed his stress ball against the wall and caught it as it came flying back to him. He tossed it again and again as he thought. He had been racking his brain for the past two weeks trying to figure out every possible way it could have played out. He could have left her, but he knew he would never do that. She was his partner, the second most important thing in his life. He had promised to protect her, to never leave her, and he would never break that promise.

They were close. He was closer to her than any other partner he'd had with the F.B.I, but he had never thought they were too close to be able to do their job. They identified the body, they caught the bad guy, and he protected her. That's what he was supposed to do.

Also, there had always been a line, it may have blurred somewhat over the years, but he had never crossed it. If the F.B.I was going to break them up anyway, then what was the point of the damn line?

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Dr. Brennan had sat down to write to clear her head, but so far all she had to show for it was a blank page.

Booth had always been overprotective of her; despite the fact that she had proved numerous times she could take care of herself. That wasn't reason enough to split them up though. They solved nearly every case they got. It just wasn't rational for the F.B.I to break up one of the best teams they had.

It wasn't like they couldn't keep it professional. They had managed that very well, she thought.

She sighed and leaned back in her chair. She couldn't do anything tonight. She would just have to wait until tomorrow and convince whoever was asking questions that she and Booth did not need to be split up.

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**A/N: Hello people. This is my first Bones fanfic, so tell me what you think, drop a review, an alert, you know anything.**


	2. Chapter 2

Angela set down a cup of coffee on her friend's desk. She sat down on the other side and said, "Don't worry Sweetie, they can't break you up."

"But Ange, they can. And they're serious about it," Brennan replied.

Angela sighed; sometimes she had to remember who she was talking to. "What I mean is, when they talk to you, they'll know that they shouldn't."

A slight smile crossed Brennan's face, "Thanks Ange."

"It's what I'm here for, Sweetie." Angela patted her friend on the shoulder. As she stood up to leave, Booth walked in.

He took her coat off the hook, walked up behind her, slipped an arm around her and helped her up, "C'mon Bones, time to go." When Booth tried to help her with her coat she took it out of his hands and put it on herself. He ushered her out of the office much as he would when taking her to court or a crime scene.

Brennan looked up at him and he gave her one of his charm smiles. Could it be possible he was not worried about this? Brennan wondered.

He was trying to be strong for her, protecting her, as he always did, Angela decided. It was just sweet, she thought.

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Booth and Brennan were sitting side by side in a nameless room in the Hoover F.B.I building. "Do you know anything about the people questioning us?" Brennan asked.

"Yeah, I called Sweets earlier today. Doctors Caitlyn Covent and Connor Hill, two of the Bureau's best psychologists, and they do this kinda thing a lot," Booth answered.

"Is that good or bad?"

"I don't know."

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Caitlyn Covent and Connor Hill showed up a few minutes later and ushered Booth and Brennan into separate rooms. Booth looked around the interrogation room he had been brought into. "Charming," he said.

He was about to continue when Caitlyn spoke. "Before you ask, no, there is no specific purpose to you being put in interrogation rooms, it is simply what we have available today. So, sit, and we'll begin."

Booth sat. "Okay, what are we gonna start with?"

"We'll start with the torched car you were called to a couple weeks ago."

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"_Come on Bones, we got ourselves a torch job," Booth said ducking under the crime scene tape and holding it up for her._

_Dr. Brennan walked directly over to the car, flipped on a flashlight, and began investigating the body that had been found inside._

"_Okay, so 9-1-1 call came in half an hour ago. Woman up in that apartment building looked out her window and saw the car burning. You know anything yet?" Booth asked._

"_Male, full grown, and there's too much flesh on the body to get anything else right now."_

_Booth walked around the car. The windows were rolled down, in the middle of January. That was strange. And a certain smell hung in the air, "Bones, you smell that?"_

"_Gasoline, inside of the car's still mostly covered in it."_

"_And that combined with the open windows, means this wasn't an accident."_

"_What exactly do the open windows prove?"_

"_It's the dead of winter, and it was supposed to snow tonight, no one in their right mind would have their windows down, but if you're gonna torch a car you need the windows down to let in fresh air. However these windows weren't down far enough to let oxygen in as fast as the fast as the fire was using it, which is probably why we have most of a body here. Anyway Bones, we have a murder."_

"_You sound far too excited about that Booth."_

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"And were you excited about it?" Caitlyn cut into his story.

"I wouldn't say excited. I wanted to be able to do my job and catch the bad guy," Booth defended his emotion.

"And spend time with Dr. Brennan? There's no need to answer that, it won't tell me anything I don't already know."

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"And, why, Dr. Brennan would you say Booth sounded excited?" Connor asked.

"Booth likes to catch the murderer. In a world with no murders he'd probably be utterly bored most of the time."

"Now you said something about there being too much flesh on the body to do a proper examination. How do you fix that?"

"Cam normally takes the body first in that case, she works with flesh."

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"_Dr. Brennan I am not done here yet." Cam said, without looking up._

"_What can you possibly be doing worthwhile with the soft tissue that's left?" Brennan asked_

"_Among other things, there's enough of the lungs here to confirm or deny death by fire."_

"_And is it death by fire?"_

"_I'm working on it, and you hovering is not helpful," Cam smiled as if she had suddenly remembered something, "I have an idea. I am done with the head. If you want you may remove the flesh, examine the skull and give it to Angela so she can work on facial reconstruction."_

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	3. Chapter 3

"So, Cam had the body, still not ready for Bones to remove the flesh, Angela had the skull, and Hodgins was trying to narrow down where exactly the gasoline came from that torched the car," Booth continued his story, "Bones was the only one with nothing to do and as such she hovered, asking everyone every five minutes if they had finished. So I took her to the diner. The rest of the squints needed some space to be able to finish."

"You two go to the diner a lot?" Caitlyn asked.

"Yeah, it's just a couple blocks from the Jeffersonian. We normally have coffee and pie, well I have pie."

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"You don't like pie, Dr. Brennan?" Connor asked.

"I don't like my fruit cooked," Brennan replied. She immediately thought of Sweets' theory that Booth was trying to seduce her by persuading her to like fruit pie, but did not tell the psychologist sitting across from her. "Anyway pretty soon after that Angela called me to say she had found a match from the facial reconstruction she had done."

"Off missing persons?"

"Actually, no. Off the D.C police database. Michael Cane, a former cop, had retired a couple months before. Booth and I went to his apartment to see what we could find."

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_Booth pushed open the door to Michael Cane's apartment. It was small, but Booth wasn't surprised, a cop's pension was next to nothing. Nothing jumped out at him until he came to a small room that looked like it was originally supposed to be the bedroom. Instead it held a desk, a laptop, and his bed was a fold-out couch in the main room. What drew his eyes though was one wall. "Bones, here's something that might be helpful," he called to his partner._

"_What is-" She stopped short when she noticed what Booth was looking at. The wall was completely covered with pictures, all of one man. "Who's he?" she asked._

_In answer Booth dropped a file in her hands. "Found it on his desk," he said._

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"And what was in the file?" Caitlyn asked.

"A double homicide Detective Cane worked four years ago," Booth answered, "From his partner at the time we learned that a man was arrested and charged with the murders, but was acquitted and that Michael wouldn't let it go. For four years he obsessed over the case, watching the guy, trying to find something he could get to stick in court. The only thing the file was missing was a current address, Cane didn't write it down anywhere, and there was only one other person who would have kept tabs on him."

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"_The prosecutor?" Brennan asked after Booth had explained his theory._

"_Yes, if anyone, other than Detective Cane that is, was keeping an eye on this man it was her," Booth replied, "She's on her way down right now, works at the U.S Attorney's office, took the case four years ago as a favor."_

"_Anyone we know?"_

"_Booth, Dr. Brennan, I hear you're close to finally getting something to stick to a certain murderer named Jason Roberts." Another voice joined their conversation._

"_Never mind," Brennan said and turned around, "Good morning Caroline."_

"_Morning Cher. Now what has Roberts done this time?"_

"_Murdered Michael Cane." Booth answered._

"_Booth, it's too soon to assume that, we haven't even talked to the guy yet." Brennan cautioned him._

"_Yeah Bones, but-"_

"_Your gut's telling you he did it."_

"_And he's the only suspect we've got right now, so I'm going to run with it."_

"_Well if you want to find him he works around here. Actually should be pulling into the Metro station three blocks over in about fifteen minutes." Caroline said._

_----------------------------__________________________________-----------------------------_

"I'll stop you here," Caitlyn said, "I have a patient in ten minutes. So we'll pick this up tomorrow same time."

"Good, and Bones?" Booth asked.

"Should be done for the day as well. Now, I want to remind you not to talk about what I've been asking you, and not to ask Dr. Brennan what she was asked."

"'Course not," Booth was already half way out the door.

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_Brennan staggered backwards when the knife made contact with her neck. Booth caught her before she could fall and gently laid her down. Her hand was still on her neck stopping the blood flow as best she could. "Someone call 9-1-1!" Booth shouted, "Bones, you're gonna be okay." He placed his had on top of hers helping to apply pressure to the deep knife wound. _

_But it wasn't enough and Booth could feel the life slowly leaving her. "Come on Bones. You're gonna make it. You can't die on me. Not now. She closed her eyes and her hand went limp, being kept where it was only by his hand on top of it. "Bones…Bones, come on." He continued, even though his better judgment knew she was dead._

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"Dad…Dad," Parker called as he gently shook his father.

Booth opened his eyes. "Parker what're you doing out of bed?" he asked.

"I could hear you and I came to check. You were having a bad dream so I woke you up."

Booth nodded. "Thanks bud. I'm sorry I woke you up. You can go back to bed now."

Parker nodded and walked back to his own room.

Booth had been having that dream for nearly two weeks now. He knew the cut hadn't been deep. He knew it only required a couple stitches and that she was back at work the same day. He continued to tell himself that, but the dreams were as bad as the first night.

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**A/N: okay, so there's that. This'll probably be done in a couple more chapters. Anyway, drop me a review or something. Till next time.**

**Oh, one last thing. I start school in a couple days. I am taking among other things, Chemistry, AP Calculus, Honors English, and Honors Spanish. So I'm not sure how much time I'll have to write.**


	4. Chapter 4

"It would appear we are to the true point of this questioning." Dr. Brennan said when she sat down in the same interrogation room she was in yesterday.

Connor nodded. "You know what I'm going to ask, so tell me."

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_Booth and Brennan had spent the last five minutes looking for Jason Roberts, with no luck. Brennan tapped her partner on the shoulder. "Booth right there, red hat," She said._

"_You sure?" he asked._

"_Positive." She started running after him without waiting for Booth. "F.B.I, we need to talk to you." She said putting a hand on Roberts' shoulder to stop him._

_Booth barely saw the flash of the knife as Roberts turned around and it caught Brennan in the neck. As she staggered backwards he steadied her with his hands on either side of her waist. "You okay?" he asked._

"_Booth, I'm fine, and he's getting away." Brennan answered._

"_You are not fine; you have a knife wound on your neck, Bones."_

"_It's not deep. I'll be fine."_

"_Well, I'm calling an ambulance."_

"_But Roberts-"_

_By now Booth couldn't even see their suspect. "We'll deal with him later. I am not leaving you."_

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"I only have one question Booth," Caitlyn began, "If you were put in the same situation again-?"

"I'd choose her, I'd always choose her." Booth answered before she even got a chance to finish her question.

Caitlyn nodded as she dissected his answer.

Booth's next memory of that case was on he chose not to share with the psychologist sitting across from him.

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"_Okay, I want a tip hotline set up, and I want his picture sent to train stations, bus terminals, airports, toll roads, anything you can think of. I don't want him being able to leave the district." Booth told the F.B.I agent on the other end of the phone._

"_Well Booth, that little adventure at the Metro station proves one thing," Caroline said as she burst into his office, completely ignoring the fact that he was on the phone._

"_Okay, call me with an update in an hour whether you've found something or not. Right now I gotta go." Booth hung up the phone and turned his attention to Caroline. "And what is it that this proves?"_

"_You are out of your mind in love with Dr. Brennan."_

"_What? No, I am not."_

"_Look me in the eyes," Caroline said, aware he was not doing so, "And tell me that again."_

"_She's my partner Caroline. I will protect her, no matter what."_

_Caroline turned and left, but Booth was sure she was aware of what he had avoided saying._

_-----------------------------------__________________________----------------------------------_

Over the next half hour Booth and Brennan explained how they finally managed to track down Jason Roberts. Caroline told them she would personally handle the case and get him convicted, without a confession if need be. In the end there was no confession, but the trial had ended two days ago and Jason Roberts was convicted.

"I have one last question for you," Caitlyn said once Booth got to the end of his story, "What is it that you find so appealing about your work at the Jeffersonian?"

"Bones can look at a skeleton and give me age, height, and gender. Cam can get DNA and run a tox screen on a smaller sample than anyone else I know, and can find a bruise on a mummy. Angela can get a face with nothing but the skull. Hodgins can tell me exactly where someone was killed. We solve the murders no one else can. I suppose that's it."

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"Just one more question Dr. Brennan and then you can go," Connor assured her, "Before Agent Booth was assigned to the Jeffersonian you requested a new agent every couple of weeks, what was different about Booth?"

Brennan thought about it for a couple minutes, trying to figure out how best to phrase her answer. It wasn't something that could be done easily. Her answer to this question would probably be key in determining whether she and Booth could stay together. "Booth's the one who took me out in to the field when no one else would. He never assumed that the only thing I was good at was lab work, or that I was cold and unfeeling. He steps aside and lets me handle the science, and concede that he is far better with people than I am. We balance each other out and a lot of times that's what catches the murderer." That was the least complicated explanation of her relationship with Booth that she could think of. There was more she wanted to say, but at the same time more she couldn't say, because saying it would mean accepting that it's true.

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**A/N: I'm thinking one more chapter. Hopefully to come out before the season premier.**

**Thanks to everyone who reviewed faved and alerted this story. :hug: for you all.**


	5. Chapter 5

Booth and Brennan walked side by side out of the Hoover F.B.I Building. Neither spoke. Brennan appeared to be turning a question over in her mind, wondering how best to ask it and Booth gave her the time to do so. "Booth," she started after a few more minutes, "What if they do it?"

"They won't," Booth replied, optimistic as always.

Brennan stopped walking. "What I mean is…I need…" Brennan looked down refusing to let him see her weakness.

Booth knew exactly what she needed. He put a finger under her chin and tilted her face up until her eyes met his. "_If_ they do, and they won't, there's an opening with the missing person's department out here. I'll still be here. We'll get coffee or something sometimes. I won't leave you, I never could."

She smiled and wrapped her arms around him. "Thank you."

"Anytime, Bones."

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The next morning Connor and Caitlyn met with the Deputy Director of the F.B.I. Sweets had refused to leave the director alone until he was allowed there too, but had been instructed not to speak. He had made his position very clear over the past two weeks.

"So, your thoughts?" the deputy director got straight to the point.

"The two are close," Caitlyn began and Connor nodded, "Too close is entirely a matter of perspective, the closeness hasn't really ever hindered their investigations."

"Up until two weeks ago." The deputy director interjected.

_Which is also entirely a matter of perspective._ Sweets though, but did not open his mouth.

"Well, yes," Caitlyn conceded, "And on that subject Agent Booth sees nothing wrong with his choice and will choose her again."

"However," Connor began, "They are without a doubt one of the best teams you have. Splitting them up has both a best case and worst case scenario, neither of which are very good. Best case scenario Agent Booth is moved to Missing Persons and does no where near as well as he does with the Jeffersonian. Dr. Brennan does what she had been doing up until Agent booth was assigned, requesting a new partner every two weeks."

"Worst case scenario," Caitlyn added, "Dr. Brennan refuses to work with anyone but Booth and we lose her help, possibly along with the rest of the Jeffersonian. We don't think they should be split up, but in the end it is your decision."

"They won't be. You two were rather convincing."

"What? That's _exactly_ what I have been saying the last two weeks!" Sweets exclaimed.

"And now, Dr. Sweets, we have a second opinion." The deputy director said.

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Booth popped the tops off two beers and handed one to Brennan. The two were celebrating the deputy director's decision. Booth smiled, but didn't say anything.

"Trying not to say 'I told you so'?" Brennan asked.

"No." Booth was defensive.

"Of course not," but the skepticism was evident in her tone.

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Brennan dropped the empty bottle from her fourth beer the recycling bin. "I should probably get home," she said.

Booth put a hand on her shoulder, "You're just a little too drunk to drive, Bones."

"Okay I'll call a cab, pick my car up in the morning."

"You could stay here if you want. I'll take the couch, you can have the bed."

"You sure?"

"Of course. Sit down. You don't have to go yet."

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**A/N: The end!**

**See I said before the season premier and I made it, by like a couple hours. Anyway, it doesn't matter.**


End file.
